Mercurial > repos > iuc > bioext_bealign

annotate bealign.xml @ 1:f9b72a376ec9 draft

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"planemo upload for repository https://github.com/davebx/bioext-gx/ commit 9a163dd8880c14f371e2603389f4951881a74b25"
author iuc
date Thu, 13 May 2021 16:57:26 +0000
parents 6ef10b28e967
children d8b6f0adaa79
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1 <?xml version="1.0"?>
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2 <tool id="bioext_bealign" name="Align sequences" version="@VERSION@.0">
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3 <description>to a reference using a codon alignment algorithm</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <version_command>bealign --version</version_command>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
1
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11 ## Some downstream tools, such as the TN-93 clustering tool and RAxML, might
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12 ## break if there are non-standard characters in the sequences or text other
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13 ## than alphanumerics in the sequence names, so we run the input dataset
f9b72a376ec9 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit 9a163dd8880c14f371e2603389f4951881a74b25"
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14 ## through a simple awk script to remove any non-IUPAC-standard nucleotides
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15 ## and replace any unwanted characters in the sequence names with underscores.
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16 ## This should not affect the actual alignment, since any non-standard character
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17 ## in the sequences is already ignored, but the possibility remains.
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18 cat '$input' | awk '{ if (\$0 ~ "^[^>]") {a = gensub(/[^ACGTURYKMSWBDHVNacgturykmswbdhvn?-]/, "", "g"); } else {a=gensub(/[^>A-Za-z0-9_]/, "_", "g"); }; print a } ' |
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19 sed 's,_\\+,_,g' > reads.fa &&
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20 bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet
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21 #if $advanced.expected_identity:
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22 --expected-identity $advanced.expected_identity
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23 #end if
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24 --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference
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25 #if $advanced.discard:
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26 $advanced.discard '$advanced.discarded_reads'
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27 #end if
1
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28 reads.fa alignment.bam
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29 ]]>
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30 </command>
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31 <inputs>
1
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32 <param name="input" type="data" format="fasta" label="Input reads" help="For the benefit of certain tools that depend on this aligner, such as the TN-93 clustering tool, this dataset's sequence names will have non-alphanumeric characters replaced with underscores, and the sequences will be restricted to the set of IUPAC nucleotide characters." />
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33 <conditional name="select_reference">
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34 <param name="reference_type" type="select">
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35 <option value="preset">Select preset</option>
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36 <option value="dataset">Use a history dataset</option>
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37 </param>
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38 <when value="preset">
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39 <param argument="--reference" type="select">
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40 <option value="HXB2_tat">HXB2 tat</option>
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41 <option value="HXB2_gag">HXB2 gag</option>
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42 <option value="HXB2_pol">HXB2 polymerase</option>
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43 <option value="HXB2_int">HXB2 integrase</option>
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44 <option value="HXB2_vif">HXB2 vif</option>
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45 <option value="HXB2_pr">HXB2 protease</option>
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46 <option value="HXB2_vpr">HXB2 vpr</option>
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47 <option value="NL4-3_prrt">NL4-3 protease and reverse transcriptase</option>
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48 <option value="HXB2_nef">HXB2 nef</option>
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49 <option value="HXB2_env">HXB2 envelope</option>
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50 <option value="HXB2_rt">HXB2 reverse transcriptase</option>
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51 <option value="HXB2_prrt">HXB2 protease and reverse transcriptase</option>
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52 <option value="HXB2_rev">HXB2 rev</option>
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53 <option value="HXB2_vpu">HXB2 vpu</option>
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54 </param>
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55 </when>
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56 <when value="dataset">
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57 <param argument="--reference" type="data" format="fasta" label="Reference sequences" />
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58 </when>
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59 </conditional>
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60 <section name="advanced" title="Advanced options" expanded="False">
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61 <param name="expected_identity" argument="--expected-identity" type="float" min="0" max="1" optional="True" label="Discard sequences that are insufficiently identical to the reference" />
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62 <param argument="--alphabet" type="select" label="Alphabet to use for alignment">
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63 <option value="codon" selected="True">Codon</option>
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64 <option value="dna">DNA</option>
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65 <option value="amino">Amino acids</option>
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66 </param>
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67 <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix">
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68 <option value="BLOSUM62" selected="True">Blocks substitution</option>
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69 <option value="DNA65">DNA, 65% expected identity</option>
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70 <option value="DNA70">DNA, 70% expected identity</option>
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71 <option value="DNA88">DNA, 88% expected identity</option>
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72 <option value="DNA80">DNA, 80% expected identity</option>
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73 <option value="DNA95">DNA, 95% expected identity</option>
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74 <option value="PAM200">PAM 200 substitution</option>
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75 <option value="PAM250">PAM 250 substitution</option>
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76 <option value="HIV_BETWEEN_F">HIV between+F</option>
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77 </param>
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78 <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" />
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79 <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" />
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80 <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" />
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81 </section>
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82 </inputs>
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83 <outputs>
1
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84 <data name="output" format="bam" from_work_dir="alignment.bam" />
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85 <data name="discarded_reads" format="fasta">
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86 <filter>advanced['discard']</filter>
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87 </data>
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88 </outputs>
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89 <tests>
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90 <test>
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91 <param name="input" ftype="fasta" value="bealign-in1.fa" />
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92 <param name="reference_type" value="dataset" />
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93 <param name="score_matrix" value="HIV_BETWEEN_F" />
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94 <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa" />
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95 <output name="output" file="bealign-out1.bam" ftype="bam" />
0
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96 </test>
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97 <test>
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98 <param name="input" ftype="fasta" value="bealign-in2.fa" />
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99 <param name="reference_type" value="dataset" />
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100 <param name="score_matrix" value="BLOSUM62" />
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101 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
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102 <output name="output" file="bealign-out2.bam" ftype="bam" />
0
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103 </test>
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104 <test>
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105 <param name="input" ftype="fasta" value="bealign-in2.fa" />
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106 <param name="reference_type" value="dataset" />
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107 <param name="expected_identity" value="0.9" />
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108 <param name="score_matrix" value="BLOSUM62" />
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109 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
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110 <output name="output" file="bealign-out3.bam" ftype="bam" />
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111 </test>
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112 </tests>
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113 <help>
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114 <![CDATA[
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115 bealign
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116 -------
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117
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118 Align sequences to a reference using a codon alignment algorithm.
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119
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120 NOTES
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121 -----
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122
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123 Reference can be one of the presets or a custom history reference.
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124 ]]></help>
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125 <expand macro="citations"/>
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126 </tool>